Let’s Encrypt will also accept 3072-bit RSA moduli. You can create a key with a 3072-bit modulus using some other tool like OpenSSL, and then I suspect there would be a way to use Windows APIs to import it or some other tool to convert it to a file format that the Windows APIs would be willing to open.
However, if your tool is directly creating the key and not providing an option to import an already-existing key, then respecting the limitations of your API makes perfect sense!